| Parameters | Input values |
|---|---|
| Folder name : | Example data |
| Sequence name : | CDH1 |
| Reference genome : | BSgenome.Hsapiens.UCSC.hg19 |
| Type of experiment : | Direct-BSP |
| Group order : | Low methylated DNA, High methylated DNA |
| Date of analysis : | 2023-06-09 17:25 |
| Parameters | Data files content |
|---|---|
| Sequence name : | CDH1 |
| Collections : | |
| Groups : | Low methylated DNA, High methylated DNA |
| Replicates : | 1, 2, 3 |
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_High methylated
DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_High methylated
DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_High methylated
DNA_3_methdata.csv
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_Low methylated
DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_Low methylated
DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example
data/CDH1/individual_results_direct/data/CDH1_Low methylated
DNA_3_methdata.csv
| chr16:68771035-68771036 | chr16:68771037-68771038 | chr16:68771045-68771046 | chr16:68771051-68771052 | chr16:68771059-68771060 | chr16:68771064-68771065 | chr16:68771073-68771074 | chr16:68771090-68771091 | chr16:68771092-68771093 | chr16:68771112-68771113 | chr16:68771138-68771139 | chr16:68771143-68771144 | chr16:68771150-68771151 | chr16:68771159-68771160 | chr16:68771182-68771183 | chr16:68771200-68771201 | chr16:68771203-68771204 | Mean | SD | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Low methylated DNA 1 | 0.00 | 0.00 | 0 | 0.00 | 0.000 | 6.00 | 0.00 | 0.00 | 0 | 0.00 | 0 | 1.69 | 1.98 | NA | NA | NA | NA | 0.74 | 1.72 |
| Low methylated DNA 2 | 13.16 | 1.33 | 0 | 1.40 | 0.000 | 3.40 | 0.00 | 0.00 | 0 | 0.00 | 0 | 23.22 | NA | NA | NA | NA | NA | 3.54 | 7.24 |
| Low methylated DNA 3 | 0.00 | 0.00 | 0 | 0.00 | 0.000 | 0.00 | 0.00 | 0.00 | 0 | 0.00 | 0 | 0.00 | NA | NA | NA | NA | NA | 0.00 | 0.00 |
| High methylated DNA 1 | 81.43 | 100.00 | 100 | 83.35 | 100.000 | 95.72 | 77.22 | 97.52 | 100 | 99.63 | 100 | 100.00 | 100.00 | NA | NA | NA | NA | 94.99 | 8.36 |
| High methylated DNA 2 | 83.50 | 100.00 | 100 | 84.08 | 100.000 | 95.84 | 77.83 | 98.55 | 100 | 99.73 | 100 | 100.00 | 100.00 | NA | NA | NA | NA | 95.35 | 7.93 |
| High methylated DNA 3 | 96.39 | 100.00 | 100 | 76.89 | 91.865 | 98.21 | 74.25 | 99.56 | 100 | 99.90 | 100 | 100.00 | 100.00 | 99.62 | 100 | 100 | 100 | 96.28 | 8.08 |
| chr16:68771035-68771036 | chr16:68771037-68771038 | chr16:68771045-68771046 | chr16:68771051-68771052 | chr16:68771059-68771060 | chr16:68771064-68771065 | chr16:68771073-68771074 | chr16:68771090-68771091 | chr16:68771092-68771093 | chr16:68771112-68771113 | chr16:68771138-68771139 | chr16:68771143-68771144 | chr16:68771150-68771151 | chr16:68771159-68771160 | chr16:68771182-68771183 | chr16:68771200-68771201 | chr16:68771203-68771204 | Mean | SD | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Low methylated DNA | 4.39 | 0.44 | 0 | 0.47 | 0.00 | 3.13 | 0.00 | 0.00 | 0 | 0.00 | 0 | 8.3 | 1.98 | NaN | NaN | NaN | NaN | 1.44 | 2.51 |
| High methylated DNA | 87.11 | 100.00 | 100 | 81.44 | 97.29 | 96.59 | 76.43 | 98.54 | 100 | 99.75 | 100 | 100.0 | 100.00 | 99.62 | 100 | 100 | 100 | 96.28 | 7.30 |
| Collection | Group | N | Methylation mean | SD | SEM | Confidence interval of 95% (±) |
|---|---|---|---|---|---|---|
| Low methylated DNA | 3 | 1.43 | 1.87 | 1.08 | 4.64 | |
| High methylated DNA | 3 | 95.54 | 0.67 | 0.38 | 1.65 |
| CpG number | CpG coordinate | Collection | Group | N | Methylation mean | SD | SEM | Confidence interval of 95% (±) |
|---|---|---|---|---|---|---|---|---|
| 1 | chr16:68771035-68771036 | Low methylated DNA | 3 | 4.39 | 7.60 | 4.39 | 18.87 | |
| 1 | chr16:68771035-68771036 | High methylated DNA | 3 | 87.11 | 8.11 | 4.68 | 20.14 | |
| 2 | chr16:68771037-68771038 | Low methylated DNA | 3 | 0.44 | 0.77 | 0.44 | 1.91 | |
| 2 | chr16:68771037-68771038 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 3 | chr16:68771045-68771046 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 3 | chr16:68771045-68771046 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 4 | chr16:68771051-68771052 | Low methylated DNA | 3 | 0.47 | 0.81 | 0.47 | 2.01 | |
| 4 | chr16:68771051-68771052 | High methylated DNA | 3 | 81.44 | 3.96 | 2.28 | 9.83 | |
| 5 | chr16:68771059-68771060 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 5 | chr16:68771059-68771060 | High methylated DNA | 3 | 97.29 | 4.70 | 2.71 | 11.67 | |
| 6 | chr16:68771064-68771065 | Low methylated DNA | 3 | 3.13 | 3.01 | 1.74 | 7.47 | |
| 6 | chr16:68771064-68771065 | High methylated DNA | 3 | 96.59 | 1.40 | 0.81 | 3.49 | |
| 7 | chr16:68771073-68771074 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 7 | chr16:68771073-68771074 | High methylated DNA | 3 | 76.43 | 1.92 | 1.11 | 4.76 | |
| 8 | chr16:68771090-68771091 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 8 | chr16:68771090-68771091 | High methylated DNA | 3 | 98.54 | 1.02 | 0.59 | 2.53 | |
| 9 | chr16:68771092-68771093 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 9 | chr16:68771092-68771093 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 10 | chr16:68771112-68771113 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 10 | chr16:68771112-68771113 | High methylated DNA | 3 | 99.75 | 0.14 | 0.08 | 0.34 | |
| 11 | chr16:68771138-68771139 | Low methylated DNA | 3 | 0.00 | 0.00 | 0.00 | 0.00 | |
| 11 | chr16:68771138-68771139 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 12 | chr16:68771143-68771144 | Low methylated DNA | 3 | 8.30 | 12.95 | 7.47 | 32.16 | |
| 12 | chr16:68771143-68771144 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 13 | chr16:68771150-68771151 | Low methylated DNA | 1 | 1.98 | NA | NA | NaN | |
| 13 | chr16:68771150-68771151 | High methylated DNA | 3 | 100.00 | 0.00 | 0.00 | 0.00 | |
| 14 | chr16:68771159-68771160 | Low methylated DNA | 0 | NaN | NA | NA | NaN | |
| 14 | chr16:68771159-68771160 | High methylated DNA | 1 | 99.62 | NA | NA | NaN | |
| 15 | chr16:68771182-68771183 | Low methylated DNA | 0 | NaN | NA | NA | NaN | |
| 15 | chr16:68771182-68771183 | High methylated DNA | 1 | 100.00 | NA | NA | NaN | |
| 16 | chr16:68771200-68771201 | Low methylated DNA | 0 | NaN | NA | NA | NaN | |
| 16 | chr16:68771200-68771201 | High methylated DNA | 1 | 100.00 | NA | NA | NaN | |
| 17 | chr16:68771203-68771204 | Low methylated DNA | 0 | NaN | NA | NA | NaN | |
| 17 | chr16:68771203-68771204 | High methylated DNA | 1 | 100.00 | NA | NA | NaN |
Student’s T test (two-samples, unpaired).
| Collection | Compared group 1 | Compared group 2 | N group 1 | N group 2 | p-value | p-value significance level |
|---|---|---|---|---|---|---|
| Low methylated DNA | High methylated DNA | 3 | 3 | 2.34e-05 | **** |
ERROR: ℹ In argument: data = map(.data$data, .f, ...).
Caused by error in map(): ℹ In index: 1. Caused by error in
t.test.default(): ! les données sont pratiquement
constantes ERROR: ℹ In argument:
data = map(.data$data, .f, ...). Caused by error in
map(): ℹ In index: 1. Caused by error in
t.test.default(): ! les données sont pratiquement
constantes ERROR: ℹ In argument:
data = map(.data$data, .f, ...). Caused by error in
map(): ℹ In index: 1. Caused by error in
t.test.default(): ! les données sont pratiquement
constantes ERROR: ℹ In argument:
data = map(.data$data, .f, ...). Caused by error in
map(): ℹ In index: 1. Caused by error in
t.test.default(): ! nombre d’observations ‘x’ insuffisant
ERROR: ℹ In argument: data = map(.data$data, .f, ...).
Caused by error in map(): ℹ In index: 1. Caused by error in
t.test.default(): ! nombre d’observations ‘x’ insuffisant
ERROR: ℹ In argument: data = map(.data$data, .f, ...).
Caused by error in map(): ℹ In index: 1. Caused by error in
t.test.default(): ! nombre d’observations ‘x’ insuffisant
ERROR: ℹ In argument: data = map(.data$data, .f, ...).
Caused by error in map(): ℹ In index: 1. Caused by error in
t.test.default(): ! nombre d’observations ‘x’ insuffisant
ERROR: ℹ In argument: data = map(.data$data, .f, ...).
Caused by error in map(): ℹ In index: 1. Caused by error in
t.test.default(): ! nombre d’observations ‘x’
insuffisant
Warning: CpG sites 3, 9, 11, 13, 14, 15, 16, 17 are removed as T test can not be performed due to N<3 for at least one group or essentially constant data between two groups.
Student’s T test (two-samples, unpaired).
| CpG number | CpG coordinate | Collection | Compared group 1 | Compared group 2 | N group 1 | N group 2 | p-value | p-value significance level |
|---|---|---|---|---|---|---|---|---|
| 1 | chr16:68771035-68771036 | Low methylated DNA | High methylated DNA | 3 | 3 | 2.14e-04 | *** | |
| 2 | chr16:68771037-68771038 | Low methylated DNA | High methylated DNA | 3 | 3 | 1.98e-05 | **** | |
| 4 | chr16:68771051-68771052 | Low methylated DNA | High methylated DNA | 3 | 3 | 5.14e-04 | *** | |
| 5 | chr16:68771059-68771060 | Low methylated DNA | High methylated DNA | 3 | 3 | 7.76e-04 | *** | |
| 6 | chr16:68771064-68771065 | Low methylated DNA | High methylated DNA | 3 | 3 | 3.15e-05 | **** | |
| 7 | chr16:68771073-68771074 | Low methylated DNA | High methylated DNA | 3 | 3 | 2.09e-04 | *** | |
| 8 | chr16:68771090-68771091 | Low methylated DNA | High methylated DNA | 3 | 3 | 3.57e-05 | **** | |
| 10 | chr16:68771112-68771113 | Low methylated DNA | High methylated DNA | 3 | 3 | 6.24e-07 | **** | |
| 12 | chr16:68771143-68771144 | Low methylated DNA | High methylated DNA | 3 | 3 | 6.58e-03 | ** |
Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.
The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).
Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.
The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).
Each points represent the methylation mean of clones or replicates
for a given CpG site.
The p-values and p-value significance levels are determined by
Kruskal-Wallis tests.
CDH1_lollipop_groups_as-is_condensed.png
CDH1_lollipop_groups_as-is_proportional.png
CDH1_meth_profile_condensed_no_p.png
CDH1_meth_profile_condensed_psign.png
CDH1_meth_profile_condensed_pval.png
CDH1_meth_profile_proportional_no_p.png
CDH1_descriptive_statistics_means.csv
CDH1_descriptive_statistics_means.xlsx
CDH1_descriptive_statistics_positions.csv
CDH1_descriptive_statistics_positions.xlsx
CDH1_methylation_table_groups.csv
CDH1_methylation_table_groups.xlsx
CDH1_methylation_table_replicates.csv
CDH1_methylation_table_replicates.xlsx